You can manually reconcile back your deleted transaction so they'll be removed from your discrepancy report and you can proceed with your reconciliation. Let me show you how.
In addition, here's an article you can read to learn more and help you understand your report: Fix beginning balance issues if you've reconciled the account in the past QuickBooks Online.
Lastly, you can read through the steps outlined in this helpful article to pull up a report after your reconciliation session: How do I view, print, or export a reconciliation report?
If there's anything else that I can help you with, please let me know in the comments below. Stay safe!
Thanks for posting an update here about your reconciliation, @userjamiehenry,
Have you tried closing the Reconcile page after making the changes? This way the entries and balances are updated when you resume the reconciliation.
You can also try opening your account in private browsing. This will help us check if this is caused by the large data in the cache. Your browsing activity will constantly stacks up without deleting the old stuff, which will likely cause QuickBooks to function poorly.
The private window will not save any history making it a good place to identify browser problems. To start incognito mode, use these keyboard shortcuts:
If you no longer see this alert in private browsing, clear the browser's cache. This will help delete the history of the browser, so you can start in a clean slate.
If the same thing happens, I recommend contacting our Support Team. Reach us during our support hours from 6:00 AM to 6:00 PM on weekdays and 6:00 AM til 3:00 PM on Saturdays.
When you're connected, provide all the information about your concern or request a viewing session with out representative.
Kindly update us again about this, as I want to make sure everything is taken care of for you. Have a good one!